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Crystal structure of a disulfide mutant glucose binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 20% PEG 6000, 50mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.01 38.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.19 α = 90 b = 36.6 β = 106.81 c = 64.82 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.12 50 100 0.063 11.2 3.2 103523 103523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.12 1.19 99.2 0.263 3.5 2.6 9230
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HPH 1.12 31.43 103510 103510 5176 100 0.159 0.159 0.158 0.1653 0.179 0.1841 RANDOM 6.996
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.34 -0.1 0.62 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_3_deg 11.859 r_dihedral_angle_4_deg 9.376 r_dihedral_angle_1_deg 5.555 r_sphericity_free 3.381 r_scangle_it 2.618 r_sphericity_bonded 1.968 r_scbond_it 1.822 r_mcangle_it 1.304 r_angle_refined_deg 1.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.749 r_dihedral_angle_3_deg 11.859 r_dihedral_angle_4_deg 9.376 r_dihedral_angle_1_deg 5.555 r_sphericity_free 3.381 r_scangle_it 2.618 r_sphericity_bonded 1.968 r_scbond_it 1.822 r_mcangle_it 1.304 r_angle_refined_deg 1.285 r_rigid_bond_restr 1.057 r_mcbond_it 0.911 r_angle_other_deg 0.889 r_mcbond_other 0.352 r_nbd_refined 0.224 r_symmetry_vdw_other 0.219 r_symmetry_vdw_refined 0.182 r_nbd_other 0.178 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.111 r_nbtor_other 0.085 r_metal_ion_refined 0.083 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2474 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction AMoRE phasing